The prospect that the Federal Housing Administration may finally require taxpayer assistance threatens to complicate efforts by the agency to provide additional housing market stimulus.

On Friday, the agency reported that its current reserves aren’t enough to cover potential losses, leaving a net worth deficit of $16.3 billion. Already, Obama administration officials have said they will increase insurance premiums that future borrowers will have to pay, and they’ll require borrowers to pay those premiums for a lot longer than in the past.

But Friday’s report could have other ramifications. Here are three:

1) The FHA’s shaky finances should torpedo any hopes of launching a new refinancing program through the FHA.

Such a proposal, admittedly, already had a weak chance of passing Congress. President Barack Obama proposed earlier this year allowing homeowners who owe more than their homes are worth to refinance into FHA-backed mortgages if they weren’t eligible for an existing program that is open to those with loans backed by Fannie or Freddie. Sen. Dianne Feinstein (D., Calif.) introduced such a bill in May, dubbed “HARP 3.0,” as it was similar in form to the revamped Home Affordable Refinance Program for Fannie and Freddie loans.

2) Higher loan limits are likely to fall—the question is how far.

Congress expanded the FHA’s maximum loan limits in 2008, to as high as $729,750 in certain markets, from a previous ceiling of $362,900. California’s share of the FHA’s loan business grew to 17% by last year, from just 2% in 2007.

After the loan caps declined modestly last year, lawmakers voted to return them to the higher levels through 2013, even as Congress allowed loan limits to fall for Fannie Mae and Freddie Mac.

The change allowed the FHA to grow its footprint in a handful of markets and marked the first time ever that the agency was able to guarantee larger loans than Fannie or Freddie. “Congress passed the worst of all deals,” said Rep. Scott Garrett (R., N.J.), by allowing the government to back larger loans than Fannie and Freddie, where private mortgage insurance covers a first-loss piece of low-down-payment mortgages.

3) Allowing down payments of just 3.5% on government-backed mortgages will face more scrutiny, though across-the-board increases in minimum down payments are unlikely.

Rep. Garrett said Friday that the FHA’s audit should make lawmakers more receptive to the idea of raising FHA down payments to 5%, a move he has unsuccessfully pushed in the past.

For their part, Obama administration officials said Friday that allowing borrowers to make down payments of 3.5% aren’t necessarily a problem, provided that loans are fully underwritten, fully amortizing 15- or 30-year loans. The FHA, they added, has a long established track record making such loans. The bigger problem facing the FHA is that the agency was left holding the bag after the private market imploded and the housing market fell 33%, dragging the economy into a recession.

A big reason Congress is unlikely to pull a lever raising down payments is that many households don’t have enough equity to buy homes, given the losses many homeowners sustained when the housing bubble burst or when stocks plunged in value three years ago.

“The only way for many Americans to come up with a down payment is to save it dollar for dollar,” said Lou Barnes, a mortgage banker in Boulder, Colo. “If you thought stocks and interest would enhance your down payment, you’re out of luck, and the great loss of household equity means your parents don’t have anything to help you out.”